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Troubleshooting and FAQ

The program will not start or is blocked

Windows says "Windows protected your PC". The program is not code-signed. Choose More info, then Run anyway.

macOS says the app cannot be opened. Start it once, then open System Settings, Privacy & Security, and choose Open Anyway next to the message about Chromascope. The command-line tools in the disk image need the same approval, one by one.

The Linux AppImage does not start. It needs FUSE. Run it with --appimage-extract-and-run instead.

I cannot rebuild on Windows. Close the running copy first, or the linker cannot replace the file.

My file does not open

A vendor file or folder gives an error about msconvert. The converter is not found. Install ProteoWizard and use File, Vendor import settings, Locate msconvert…, see Vendor files.

An mzML file is refused. The error names the problem. Files are checked while they are read, but a thorough check of every possible mzML defect is not complete, so a damaged file may fail late. Try the file in another tool or convert it again.

The trace is empty or missing

  • Apply XIC does nothing. Both the Target m/z and the Tolerance must be numbers above zero.
  • The XIC is flat. Check the polarity, the MS level and the acquisition type under Trace settings, and widen the tolerance. A tolerance of 10 ppm is only 0.007 at m/z 700.
  • "No matching scans". A precursor filter accepts scans within 0.01 Da of the value you typed. Choose a precursor that is listed for the file. SIM and MRM traces need spectra; a file that holds only stored chromatograms has none.
  • Peaks look different after smoothing. Smoothing changes the picture and the viewer's integration. Set Smoothing to 0 for unsmoothed numbers. Batch quantification always integrates unsmoothed data.

A number looks wrong

  • The area is negative. A baseline can lie above the signal between your boundaries. Negative areas are kept, not clipped, so you can see the problem.
  • The batch area differs from the Data explorer area. They are independent calculations: the batch uses unsmoothed traces and its own detection settings. Compare the boundaries first.
  • A concentration is missing. Missing, failed and pending areas stay empty and are never counted as zero. Look at the flags next to the sample and at the calibration range.
  • A QC rule says indeterminate. The evidence the rule needs is absent. Acknowledging a review records your reason but never turns a failure into a pass.

Saved work

A session will not reopen its files. The source files must be at their original paths. Missing runs are reported and the measurements you made remain available.

Where are my preferences? In settings.json, see Settings.

Questions

Does Chromascope send my data anywhere? No. Vendor conversion runs on your computer. The only network use of the desktop program is the once-a-day update check, which sends an ordinary web request and nothing from your work.

Can I use it for regulated work? It has not been validated on instruments and it does not certify compliance.

Does it contain an AI? No. If you connect an assistant over MCP, the assistant is a separate program of your choice. See AI assistants.

Where do I report a problem? Open an issue at github.com/chromascope-ms/chromascope/issues. Say which version you use (File, then About Chromascope…) and what you did.